As with many of Apple’s App Store changes, controversy has erupted in the wake of the company’s new in-app subscription billing, which has claimed another high-profile developer who has penned an open letter to Cupertino over their rejection.

AppleInsider is reporting that Apple’s App Store rejection police have struck again, this time in the form of Readability, the iOS version of the website service designed to make website reading easier. Last Friday, the Readability app -- which is based on Marco Arment’s popular Instapaper -- was rejected “for not adhering to the company’s new subscription policies.”

In particular, the app failed to conform to section 11.2 of the App Store Review Guidelines, which prevent iOS software from “utilizing a system other than the In App Purchase API (IAP) to purchase content, functionality or other services in an app.”

The problem stems from how the new Readability service works: The company now charges a minimum of $5 per month, keeping 30 percent and giving the remaining 70 percent to content publishers, based on what’s being read through the service. The iOS app was intended to be free for these subscribers.

Ironically, that’s the same business model that Apple is already using for their iOS and Mac App Stores, and now the company is finally enforcing guidelines on in-app purchases that have been in place for some time -- which has raised the ire of the Readability developers, not to mention many others in the iOS community.

"We're obviously disappointed by this decision, and surprised by the broad language," Readability creator Rich Ziade wrote in an open letter to Apple on the company’s blog Monday. "By including 'functionality, or services,' it's clear that you intend to pursue any subscription-based apps, not merely those of services serving up content."

While assumptions are being made that apps ranging from Dropbox and Evernote to Hulu Plus and Netflix will now be forced to give 30 percent of their subscription fees to Apple, it appears that Cupertino still has some explaining to do where “Software as a Service” apps are concerned. A MacRumors reader fired off an e-mail to Apple CEO Steve Jobs on the subject and got a typically vague response.

Based on that brief reply, it would appear that apps such as Dropbox and Evernote will be off the hook, while a service like Readability appears to be right on the edge. Time will tell, but for now Apple’s new subscription policies are creating more headaches than they are convenience for many.